Cytoscape and graphNEL

This vignette will show you how to convert networks between graphNEL and Cytoscape.

Installation

if(!"RCy3" %in% installed.packages()){
    install.packages("BiocManager")
    BiocManager::install("RCy3")
}
library(RCy3)

Required Software

The whole point of RCy3 is to connect with Cytoscape. You will need to install and launch Cytoscape:

• Download the latest Cytoscape from http://www.cytoscape.org/download.php
• Complete installation wizard
• Launch Cytoscape

cytoscapePing()

From graphNEL to Cytoscape

The graph package is a popular network tool among R users. With RCy3, you can easily translate graphNEL networks to Cytoscape networks!

Create a simple GraphNEL object

g <- makeSimpleGraph()

Now pass it along to Cytoscape:

createNetworkFromGraph(g,"myGraph")

From Cytoscape to GraphNEL

Inversely, you can use createGraphFromNetwork() in RCy3 to retreive vertex (node) and edge data.frames to construct a GraphNEL object.

g2 <- createGraphFromNetwork("myGraph")

Compare the round-trip result for yourself…

g
g2